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| author | Bryan Bishop <kanzure@gmail.com> | 2010-12-01 20:55:34 -0800 |
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| committer | Bryan Bishop <kanzure@gmail.com> | 2010-12-01 20:55:34 -0800 |
| commit | 0f7711de75de0db235702a7e683e57867e1fb64e (patch) | |
| tree | b882a7dea35173e3b8f171c320e1eaf1aa7a95fc /cad/plugins/DNA/zdna-bases/NOTES | |
| parent | 457a4c736e0aeaf7ec8e2c5e3df5e4b401b7f61a (diff) | |
| download | nanoengineer-0f7711de75de0db235702a7e683e57867e1fb64e.tar.gz nanoengineer-0f7711de75de0db235702a7e683e57867e1fb64e.zip | |
Moving files in preparation for merge.
Diffstat (limited to 'cad/plugins/DNA/zdna-bases/NOTES')
| -rwxr-xr-x | cad/plugins/DNA/zdna-bases/NOTES | 64 |
1 files changed, 64 insertions, 0 deletions
diff --git a/cad/plugins/DNA/zdna-bases/NOTES b/cad/plugins/DNA/zdna-bases/NOTES new file mode 100755 index 000000000..e60bcf1bf --- /dev/null +++ b/cad/plugins/DNA/zdna-bases/NOTES @@ -0,0 +1,64 @@ + + Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details. +----- +5/11/2007 +NOTE: I've since changed the eight nucleotide files by hand to add an oxygen to +the 3' carbon (where a bond point used to be), and removed the oxygen from the +phosphate (where a bond point is now.) This configuration is more standard in +the world of PDBs, GROMACS, and NAMOT, and is, in fact how the zdna.pdb file is +set up. + +So the prepare.py script is out-of-date and will re-generate the old files if +run. Note that prepare.py is not typically run, but is documentation about how +the files where originally generated. + +This change does make a chemical difference in that there should be an oxygen +bonded to the 3' carbon at the top of a 3'-to-5' strand (previously there was +not.) Technically, when the strands are generated, the oxygen should also be +hydrogenated *and* there should be no phosphate at the top of the 5'-to-3' +strand - but this change makes the nucleotides by themselves conform to +standards at least. +--Brian. +----- + + +Here is where I am getting my information from: +http://chemistry.gsu.edu/glactone/PDB/DNA_RNA/dna.html + +Here is how I prepared the bases information for Z-DNA. Something +along these lines should work for many different kinds of sequence +generators so this is useful info. + +I started with zdna.pdb, a file I found on the Internet. I wanted to +do three things: separate the two strands, convert from PDB to MMP +format, and add bonding information which was absent in the zdna.pdb +file. + +Adding the bonding information required putting bond inference into +the _readpdb function in files_pdb.py, and the actual work is done +in the inferBonds function in bonds.py. Once this was done, the +conversion from PDB to MMP was just a matter of importing the PDB +file into nE-1 and saving it as two MMP files, one for each strand. + +I separated the strands by double-clicking on an atom in select atoms +mode, so that the whole strand got selected by transitivity. Then I +could delete the selected strand and save the result as my MMP file. + +The next step was to group the atoms in strand1.mmp by what base they +were a member of. I did this grouping by changing the drawing modes +for the atoms in every other base from default to lines. Using +strand1.mmp and starting at the 5' end, I did this and saved the +result as the file strund1.mmp. This part is where human judgement is +required to decide where to put the divisions between building blocks. + +The next step is heavily automated, and is done by the prepare.py +script. The groups are written out to a series of individual MMP +files. These files (with names like "cytosine-inner.mmp") are used +by nE-1's DNA generator to build new structures. + +As I write this, there is a remaining flaw in prepare.py. It should +put bondpoints on the two dangling bonds on each base. For bases in +the middle of a strand, these bondpoints will be joined with those of +the adjacent bases. There will be two bondpoints left on the ends, +and ideally we should attach a hydrogen at the 5' end and a hydroxyl +at the 3' end. |